Who says those things need to be nacelles?
"Take a good look at this, people. It says something about this ship. It says that we will fight, and we will keep on fighting, until we can't fight any more!"
(I get it, they probably wouldn't keep phaser cells in the shuttlebay.)
But the way they mount nacelles on most starships implies easy replacement. Maybe those are the cores of the nacelles, and get replaced by sliding them out of their housings like jet fighter engines. You could even say some are warp-capable while others are not, which may explain some discrepancies over the years.
Mark